Refining Dynamics of Gene Regulatory Networks in a Stochastic π-Calculus Framework

Loïc Paulevé (1) , Morgan Magnin (1) , Olivier Roux (2)

1 IRCCyN - Institut de Recherche en Communications et en Cybernétique de Nantes
2 MeForBio

In this paper, we introduce a framework allowing to model and analyse efficiently Gene Regulatory Networks in their temporal and stochastic aspects. The analysis of stable states and inference of René Thomas' discrete parameters derives from this logical formalism. We offer a compositional approach which comes with a natural translation to the Stochastic π-Calculus. The method we propose consists in successive refinements of generalized dynamics of Gene Regulatory Networks. We apply this method to the control of the differentiation in a Gene Regulatory Network generalizing metazoan segmentation processes.

Mots clés: Stochastic pi-calculus; Gene regulatory networks; Temporal and stochastic parameters; René Thomas' parameters inference; Stochastic pi-calculus.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Modélisation et simulation

Loïc Paulevé, Morgan Magnin, Olivier Roux. Refining Dynamics of Gene Regulatory Networks in a Stochastic π-Calculus Framework. Transactions on Computational Systems Biology, 2011, XIII, pp.171-191. ⟨10.1007/978-3-642-19748-2_8⟩. ⟨hal-00397235v2⟩